Gene loci information

Transcript annotation

  • This transcript has been annotated as Cystathionine beta-synthase.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g13123 g13123.t3 TSS g13123.t3 28045997 28045997
chr_1 g13123 g13123.t3 isoform g13123.t3 28046065 28048905
chr_1 g13123 g13123.t3 exon g13123.t3.exon1 28046065 28046241
chr_1 g13123 g13123.t3 exon g13123.t3.exon2 28047860 28047966
chr_1 g13123 g13123.t3 cds g13123.t3.CDS1 28047906 28047966
chr_1 g13123 g13123.t3 exon g13123.t3.exon3 28048027 28048905
chr_1 g13123 g13123.t3 cds g13123.t3.CDS2 28048027 28048904
chr_1 g13123 g13123.t3 TTS g13123.t3 28049656 28049656

Sequences

>g13123.t3 Gene=g13123 Length=1163
ATGTCTGAGAGTAAAGAAAGTGCAATGAATGGACATCAATCAACATGTTCAACACATTTG
AAGTACAAGGCACTTGATATGCCTGAAACTTTGCAACCTGACTTTGTTTATCCAGATGAA
CCATCAAAATGTACTTGGGTTCGCGATAAATCTAAACAAACTGCAACTCCACATACTCCA
TGAAAGGCCAAAAACAATTCCTCATATTTTGGATGCAATCGGTATGACACCAATGGTAAA
ATTGAACAAAATCCCACAATCATTGGGCATTAAATGTCAAATGTACGCAAAGTGTGAATT
CTTGAATCCAGGTGGTTCTGTCAAAGATCGAATTGGTTATCGCATGGTACTTGATGCTGA
AGAAAAAGGTTTACTCAAGCCAGGATATACAATTATTGAGCCAACATCAGGAAATACAGG
AATTGGCTTAGCTATGGCAAGTGCAGTTCGTGGTTATCGCTGCATTATCGTTTTGCCTGA
GAAAAATTCAGATGAAAAAGTCAATGCACTCAAGGCATTTGGAGCAGAAATAATTCGTAC
AAGAACTGAAGCTAAATTCGATGAGCCTGATTCATTAGTCGCTGTTGCTCAACGCTTGCA
GAAAGAAATTCCAAACTCTGTCATTTTAAATCAATACACAAATTGCGGCAATCCATTGGC
TCATTATGATGGAACTGGAAGTGAAATTTTGTATCAATTGGATGGAAAAGTTGATATGGT
CGTGCTTGGAGCAGGAACAGGCGGAACAATAACTGGTGTAGGTCGTCGAATTAAAGAAGA
ATGTCCCAATTGCAAAATTATTGGAGTTGACCCAGAAGGTTCAATTTTAGCACAACCAGA
TTCTTTGAATAAAACGGATGTTGTGGTTTTTGATGTCGAAGGCATCGGTTACGATTTTAT
TCCGACTGTTCTAGATCGCGATATTGTTGATAAATGGATCAAATCTAATGATAAGATGGC
TTTTCCAATGGCAAAACGTCTAATTCGCGAAGAAGGCTTTTTATGTGGTGGTTCATCTGG
TGCAGCAATGGCAGCTGCAATCGAAGTCGCTAAAGATTTATCAGAAGATCAAGTTTGTGT
TGTCATTTGTCCGGACAATATTCGTAATTACATGAGTAAATTTTTGGTTGACAATTGGAT
GGAAGCAAGAGGTTTGAAAGAAT

>g13123.t3 Gene=g13123 Length=313
MTPMVKLNKIPQSLGIKCQMYAKCEFLNPGGSVKDRIGYRMVLDAEEKGLLKPGYTIIEP
TSGNTGIGLAMASAVRGYRCIIVLPEKNSDEKVNALKAFGAEIIRTRTEAKFDEPDSLVA
VAQRLQKEIPNSVILNQYTNCGNPLAHYDGTGSEILYQLDGKVDMVVLGAGTGGTITGVG
RRIKEECPNCKIIGVDPEGSILAQPDSLNKTDVVVFDVEGIGYDFIPTVLDRDIVDKWIK
SNDKMAFPMAKRLIREEGFLCGGSSGAAMAAAIEVAKDLSEDQVCVVICPDNIRNYMSKF
LVDNWMEARGLKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13123.t3 CDD cd01561 CBS_like 2 298 2.21181E-125
7 g13123.t3 Gene3D G3DSA:3.40.50.1100 - 2 299 1.0E-128
6 g13123.t3 Gene3D G3DSA:3.40.50.1100 - 31 144 1.0E-128
2 g13123.t3 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 2 309 8.7E-166
3 g13123.t3 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 2 309 8.7E-166
1 g13123.t3 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 2 289 8.0E-67
5 g13123.t3 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. 23 41 -
4 g13123.t3 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 2 310 4.58E-96
8 g13123.t3 TIGRFAM TIGR01137 cysta_beta: cystathionine beta-synthase 2 311 1.9E-155

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0019343 cysteine biosynthetic process via cystathionine BP
GO:0006535 cysteine biosynthetic process from serine BP
GO:0004122 cystathionine beta-synthase activity MF
GO:0005737 cytoplasm CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed